C. diff uses toxic compound to fuel growth advantage

(Press-News.org) The pathogen C. diff — the most common cause of health care-associated infectious diarrhea — can use a compound that kills the human gut’s resident microbes to survive and grow, giving it a competitive advantage in the infected gut. 

A team led by investigators at Vanderbilt University Medical Center has discovered how C. diff (Clostridioides difficile) converts the poisonous compound 4-thiouracil, which could come from foods like broccoli, into a usable nutrient. Their findings, published March 25 in the journal Cell Host & Microbe, increase understanding of the molecular drivers of C. diff infection and point to novel therapeutic strategies. 

C. diff causes about half a million infections in the U.S. each year, according to the Centers for Disease Control and Prevention. Factors that increase risk of C. diff infection include antibiotic use, age over 65, and recent stays in hospitals and other health care facilities. 

Like other pathogens, C. diff must acquire nutrients to survive and grow. 

“We’re interested in trying to understand the nutrients that C. diff needs during infection, and how what you eat influences what C. diff eats in your gut,” said the study’s first author, Matthew Munneke, a graduate student working with Eric Skaar, PhD, MPH, the Ernest W. Goodpasture Professor of Pathology and director of the Vanderbilt Institute for Infection, Immunology and Inflammation. 

The group focused on nucleotides — the building blocks of DNA and RNA — which are a class of nutrients that hasn’t been well studied for C. diff. 

The researchers found that C. diff must acquire a certain type of nucleotides (pyrimidines) to cause infection, and they discovered an enzyme they named TudS (thiouracil desulfurase) that C. diff uses to salvage the pyrimidine nucleotide uracil from a related compound: 4-thiouracil. 

They showed that 4-thiouracil gets incorporated into RNA and is toxic to resident gut microbes that do not have the TudS enzyme. In C. diff, however, TudS modifies and detoxifies 4-thiouracil, making it available as a nutrient. The researchers demonstrated that TudS contributes to C. diff “fitness” in mice fed 4-thiouracil and in a novel MiniBioreactor model that contains a community of bacteria isolated from human feces with added 4-thiouracil. 

“We think that 4-thiouracil metabolism is beneficial to C. diff because it acts as a nutrient to fuel the bacteria, and it also may inhibit neighboring bacteria, which would give C. diff a further competitive advantage within the gut environment,” Munneke said. 

The TudS enzyme may represent a novel therapeutic target for treating C. diff infections. It is not present in many resident gut microbes (or in human cells), so an antimicrobial targeting it to kill C. diff might help preserve the healthy gut microbiota, he noted. 

The researchers also showed that adding C. diff TudS to a probiotic strain of E. coli blunted C. diff’s fitness advantage in an in vitro model. 

“It might be possible to use a probiotic with this enzyme to diminish C. diff’s ability to thrive in the gut and push it out,” Munneke said. 

Although the researchers showed that 4-thiouracil is present in the human gut, the source of this compound is unclear. Livestock that consume a diet rich in cruciferous vegetable family members (such as kale and other leafy greens, broccoli and cauliflower) have elevated levels of 4-thiouracil, and it is present in broccoli, both suggestive that a dietary source may contribute to the presence of 4-thiouracil in the human gut. 

“More research is needed to understand the source of 4-thiouracil, but if it comes from the diet, that could inform dietary interventions for C. diff infection,” Munneke said. 

It’s not time to give up eating cruciferous vegetables though. In the healthy gut, some resident microbes contain a TudS-related enzyme and can likely convert 4-thiouracil into nutrients. These microbes may be missing in the C. diff-infected gut, Munneke said. 

Other VUMC authors of the Cell Host & Microbe paper are Catherine Shelton, PhD, Darian Carroll, PhD, Nicole Kirchoff, PhD, Martin Douglass, PhD, M. Wade Calcutt, PhD, Katherine Gibson-Corley, DVM, PhD, Maribeth Nicholson, MD, MPH, and Mariana Byndloss, DVM, PhD. Collaborators at the University of Florida and Baylor College of Medicine contributed to the studies. 

The research was supported by grants from the National Institutes of Health (R01AI164587, U19AI174999, R01GM070641, T32ES007028, F31AI172352, K23AI156132, U19AI157981).  

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